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- PDB-4ib2: Crystal structure of a putative lipoprotein (RUMGNA_00858) from R... -

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Basic information

Entry
Database: PDB / ID: 4ib2
TitleCrystal structure of a putative lipoprotein (RUMGNA_00858) from Ruminococcus gnavus ATCC 29149 at 1.76 A resolution
ComponentsPutative Lipoprotein
KeywordsTRANSPORT PROTEIN / putative methionine-bindning / NLPA lipoprotein / PF03180 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyLipoprotein NlpA family / NlpA lipoprotein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / membrane / Alpha Beta / METHIONINE / Lipoprotein
Function and homology information
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative lipoprotein (RUMGNA_00858) from Ruminococcus gnavus ATCC 29149 at 1.76 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Lipoprotein
B: Putative Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,24517
Polymers55,2592
Non-polymers98615
Water6,161342
1
A: Putative Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1058
Polymers27,6291
Non-polymers4757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1409
Polymers27,6291
Non-polymers5118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.099, 52.454, 54.908
Angle α, β, γ (deg.)99.810, 87.500, 94.960
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative Lipoprotein /


Mass: 27629.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Strain: ATCC 29149 / Gene: ZP_02040096.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7AZY4
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 28-278 OF THE TARGET SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.8M (NH4)2SO4, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 9, 2010
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→40.876 Å / Num. obs: 41851 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.456 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.76-1.820.5622.415284391493.5
1.82-1.90.3993.317710451095.2
1.9-1.980.2814.715055384195.2
1.98-2.090.1956.717216438995.6
2.09-2.220.143916231413596
2.22-2.390.1041216309418396.3
2.39-2.630.07516.416345417496.8
2.63-3.010.05223.216452421797.1
3.01-3.780.02937.916136416997
3.780.0251.816823431998

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
XSCALEJanuary 30, 2009data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→40.876 Å / Cor.coef. Fo:Fc: 0.9584 / Cor.coef. Fo:Fc free: 0.9502 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (- ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). 4. CHLORIDE (CL) AND GLYCEROL (GOL) FROM THE PURIFICATION AND CRYOPROTECTANT SOLUTION ARE MODELED. 5. ENDOGENOUS METHIONINE (MET) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON ELECTRON DENSITY AND COMPARISON WITH OTHER SIMILAR PROTEIN STRUCTURES AND IS LIKELY THE NATURAL LIGAND.
RfactorNum. reflection% reflectionSelection details
Rfree0.1844 2110 5.04 %RANDOM
Rwork0.1619 ---
obs0.163 41847 96.12 %-
Displacement parametersBiso max: 122.21 Å2 / Biso mean: 30.3081 Å2 / Biso min: 9 Å2
Baniso -1Baniso -2Baniso -3
1--3.7639 Å22.597 Å2-0.3676 Å2
2--2.0682 Å21.852 Å2
3---1.6956 Å2
Refine analyzeLuzzati coordinate error obs: 0.233 Å
Refinement stepCycle: LAST / Resolution: 1.76→40.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 0 51 342 4184
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1897SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes574HARMONIC5
X-RAY DIFFRACTIONt_it3999HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion540SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5110SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3999HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5449HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.75
X-RAY DIFFRACTIONt_other_torsion2.77
LS refinement shellResolution: 1.76→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 155 5.16 %
Rwork0.2101 2851 -
all0.2106 3006 -
obs--96.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59840.168-0.02292.6140.19820.67450.00630.02630.0212-0.02770.0372-0.1789-0.07450.0418-0.04350.0217-0.04150.0254-0.0657-0.0199-0.048218.944317.190542.3521
20.56850.0840.03532.2993-0.25750.874-0.01180.0617-0.07860.01540.00770.18890.0751-0.05370.00410.0284-0.03320.0285-0.0709-0.0325-0.0239.3934-6.176942.6588
30.5741-0.78340.89911.6248-1.81035.6845-0.05980.09250.1421-0.0058-0.118-0.1314-0.56060.45680.17770.0706-0.10080-0.1248-0.0088-0.183919.5659-5.355214.0209
40.6226-0.0405-0.42341.3407-0.99382.7094-0.01440.1119-0.0527-0.48440.15890.29570.4915-0.2556-0.14450.19-0.0865-0.0687-0.1776-0.0025-0.18489.64-27.882418.0824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|32 - A|116 A|234 - A|278 }A32 - 116
2X-RAY DIFFRACTION1{ A|32 - A|116 A|234 - A|278 }A234 - 278
3X-RAY DIFFRACTION2{ A|117 - A|233 }A117 - 233
4X-RAY DIFFRACTION3{ B|36 - B|116 B|234 - B|278 }B36 - 116
5X-RAY DIFFRACTION3{ B|36 - B|116 B|234 - B|278 }B234 - 278
6X-RAY DIFFRACTION4{ B|117 - B|233 }B117 - 233

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